Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

Eugenio Azpeitia, Nathan Weinstein, Mariana Benítez, Luis Mendoza, Elena R. Alvarez-Buylla

Over the last few decades, the Arabidopsis thaliana root stem cell niche (RSCN) has become a model system for the study of plant development and stem cell niche dynamics. Currently, many of the molecular mechanisms involved in RSCN maintenance and development have been described. A few years ago, we published a gene regulatory network (GRN) model integrating this information. This model suggested that there were missing components or interactions. Upon updating the model, the observed stable gene configurations of the RSCN could not be recovered, indicating that there are additional missing components or interactions in the model. In fact, due to the lack of experimental data, GRNs inferred from published data are usually incomplete. However, predicting the location and nature of the missing data is a not trivial task. Here, we propose a set of procedures for detecting and predicting missing interactions in Boolean networks. We used these procedures to predict putative missing interactions in the A. thaliana RSCN network model. Using our approach, we identified three necessary interactions to recover the reported gene activation configurations that have been experimentally uncovered for the different cell types within the RSCN: (1) a regulation of PHABULOSA to restrict its expression domain to the vascular cells, (2) a self-regulation of WOX5, possibly by an indirect mechanism through the auxin signaling pathway, and (3) a positive regulation of JACKDAW by MAGPIE. The procedures proposed here greatly reduce the number of possible Boolean functions that are biologically meaningful and experimentally testable and that do not contradict previous data. We believe that these procedures can be used on any Boolean network. However, because the procedures were designed for the specific case of the RSCN, formal demonstrations of the procedures should be shown in future efforts.